Russian version English version
Volume 18   Issue 1   Year 2023
Bessonova T.A.1, Rybina A.A.2, Marakulina D.A.1,3, Kaznadzey A.D.4, Gelfand M.S.2,4, Ozoline O.N.1, Tutukina M.N.1,2,4

Phylogeny and cross-regulation of the YjjM and LeuO transcription factors translated as multiple protein forms from one gene in Escherichia coli

Mathematical Biology & Bioinformatics. 2023;18(1):1-14.

doi: 10.17537/2023.18.1.


  1. Jacob F., Monod J. Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology. 1961;3:318–356. doi: 10.1016/S0022-2836(61)80072-7
  2. Jacob F., Perrin D., Sanchez C., Monod J. Operon: a group of genes with the expression coordinated by an operator. Comptes Rendus Hebdomadaires des Séances de l'Académie des Sciences. 1960;250:1727–1729.
  3. Busby S.J.W. Transcription activation in bacteria: ancient and modern. Microbiology. 2019;165(4):386–395. doi: 10.1099/mic.0.000783
  4. Shimada T., Bridier A., Briandet R., Ishihama A. Novel roles of LeuO in transcription regulation of E. coli genome: antagonistic interplay with the universal silencer H-NS. Molecular Microbiology. 2011;82(2):378–397. doi: 10.1111/j.1365-2958.2011.07818.x
  5. Ishihama A., Shimada T., Yamazaki Y. Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic Acids Research. 2016;44(5):2058–2074. doi: 10.1093/nar/gkw051
  6. Tucker A.C., Escalante-Semerena J.C. Biologically active isoforms of CobB sirtuin deacetylase in Salmonella enterica and Erwinia amylovora. Journal of Bacteriology. 2010;192(23):6200–6208. doi: 10.1128/JB.00874-10
  7. Umehara T., Kosono S., Söll D., Tamura K. Lysine Acetylation Regulates Alanyl-tRNA Synthetase Activity in Escherichia coli. Genes (Basel). 2018;9(10):473. doi: 10.3390/genes9100473
  8. Di Martino M.L., Romilly C., Wagner E.G.H., Colonna B., Prosseda G. One Gene and Two Proteins : a Leaderless mRNA Supports the Translation of a Shorter Form of the Shigella VirF Regulator. mBio. 2016;7(6):1–10. doi: 10.1128/mBio.01860-16
  9. Prosseda G., Falconi M., Giangrossi M., Gualerzi C. O., Micheli G., Colonna B. The virF promoter in Shigella: More than just a curved DNA stretch. Molecular Microbiology. 2004;51(2):523–537.  doi: 10.1046/j.1365-2958.2003.03848.x
  10. Pérez-Rueda E., Collado-Vides J., Segovia L. Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Computational Biology and Chemistry. 2004;28(5–6):341–350. doi: 10.1016/j.compbiolchem.2004.09.004
  11. Suvorova I.A., Tutukina M.N., Ravcheev D.A., Rodionov D.A., Ozoline O.N., Gelfand M.S. Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria. Journal of Bacteriology. 2011;193(15):3956–3963. doi: 10.1128/JB.00277-11
  12. Henikoff S., Haughn G.W., Calvo J.M., Wallace J.C. A large family of bacterial activator proteins. Proceedings of the National Academy of Sciences of the United States of America. 1988;85(18):6602–6606. doi: 10.1073/pnas.85.18.6602
  13. Hertzberg K.M., Gemmill R., Jones J., Calvo J.M. Cloning of an EcoRI-generated fragment of the leucine operon of Salmonella typhimurium. Gene. 1980;8(2):135–152. doi: 10.1016/0378-1119(80)90033-5
  14. Hernández-Lucas I., Calva E. The coming of age of the LeuO regulator. Molecular Microbiology. 2012;85(6):1026–1028. doi: 10.1111/j.1365-2958.2012.08175.x
  15. Dillon S.C., Espinosa E., Hokamp K., Ussery D.W., Casadesús J., Dorman C.J. LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium. Molecular Microbiology. 2012;85:1072–1089. doi: 10.1111/j.1365-2958.2012.08162.x
  16. Hernández-Lucas I., Gallego-Hernández A.L., Encarnación S., Fernández-Mora M., Martínez-Batallar A.G., Salgado H., Oropeza R., Calva E. The LysR-type transcriptional regulator LeuO controls expression of several genes in Salmonella enterica serovar Typhi. Journal of Bacteriology. 2008;190(5):1658–1670. doi: 10.1128/JB.01649-07
  17. NCBI RefSeq FTP.  (accessed 20.01.2023).
  18. FTP EMBL-EBI. (accessed 20.01.2023).
  19. FTP UniProt. (accessed 20.01.2023).
  20. FTP NCBI. (accessed 20.01.2023).
  21. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. Journal of Molecular Biology. 1990;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2
  22. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079. doi: 10.1093/bioinformatics/btp352
  23. Huerta-Cepas J., Szklarczyk D., Heller D., Hernández-Plaza A., Forslund S.K., Cook H., Mende D.R., Letunic I., Rattei T., Jensen L.J., von Mering C., Bork P. eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research. 2019;47(D1):D309–D314. doi: 10.1093/nar/gky1085
  24. Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research. 2002;30(14):3059–3066. doi: 10.1093/nar/gkf436
  25. Price M.N., Dehal P.S., Arkin A.P. FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix. Molecular Biology and Evolution. 2009;26(7):1641–1650. doi: 10.1093/molbev/msp077
  26. Steinegger M., Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology. 2017;35:1026–1028. doi: 10.1038/nbt.3988
  27. Cock P.J., Antao T., Chang J.T., Chapman B.A., Cox C.J., Dalke A., Friedberg I., Hamelryck T., Kauff F., Wilczynski B., de Hoon M.J. L. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25(11):1422–1423. doi: 10.1093/bioinformatics/btp163
  28. Letunic I., Bork P. Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Research. 2021;49(W1):W293–W296. doi: 10.1093/nar/gkab301
  29. Zulkower V., Rosser S. DNA Features Viewer: A sequence annotation formatting and plotting library for Python. Bioinformatics. 2020;36(15):4350–4352. doi: 10.1093/bioinformatics/btaa213
  30. TEC database. (accessed 20.01.2023).
  31. Zhang Y., Liu T., Meyer C.A., Eeckhoute J., Johnson D.S., Bernstein B.E., Nusbaum C., Myers R.M., Brown M., Li W., Liu X.S. Model-based analysis of ChIP-Seq (MACS). Genome Biology. 2008;9. Article No. R137. doi: 10.1186/gb-2008-9-9-r137
  32. Quinlan A.R., Hall I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–842. doi: 10.1093/bioinformatics/btq033
  33. Bailey T.L., Johnson J., Grant C.E., Noble W.S. The MEME Suite. Nucleic Acids Research. 2015;43(W1):W39–W49. doi: 10.1093/nar/gkv416
  34. Lee D.J., Bingle L.E.H., Heurlier K., Pallen M.J., Penn C.W., Busby S.J.W., Hobman J.L. Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains. BMC Microbiology. 2009;9(252):1–14 doi: 10.1186/1471-2180-9-252
  35. Laemmli U.K. Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4. Nature. 1970;227:680–685. doi: 10.1038/227680a0
  36. Igarashi K., Ishihama A. Bipartite functional map of the E. coli RNA polymerase alpha subunit: involvement of the C-terminal region in transcription activation by cAMP-CRP. Cell. 1991;65(6):1015–1022. doi: 10.1016/0092-8674(91)90553-B
  37. Purtov Y.A., Glazunova O.A., Antipov S.S., Pokusaeva V.O., Fesenko E.E., Preobrazhenskaya E.V., Shavkunov K.S., Tutukina M.N., Lukyanov V.I., Ozoline O.N. Promoter islands as a platform for interaction with nucleoid proteins and transcription factors. Journal of Bioinformatics and Computational Biology. 2014;12(2):1441006. doi: 10.1142/S0219720014410066
  38. Yang D., Dong J., Su X., Zhang W., Zhang L., Li L., Lv L., Guo L. Functional analysis of the uropathogenic Escherichia coli R049 gene. Microbiological Research. 2015;171:39–44. doi: 10.1016/j.micres.2015.01.002
  39. Regulon DB Database. (accessed 20.01.2023).
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2023.18.1
published in English

Abstract (eng.)
Abstract (rus.)
Full text (eng., pdf)
Supplementary data


  Copyright IMPB RAS © 2005-2024